Yeah, the sync issue definitely exists if it (or anything else) is running from the music partition. You can work around it by selecting emphatic in the hijack menu, and then telling emphatic to Quit. (Obviously 'Close' doesn't help).

[Edit]... and if you used EXEC (as suggested) rather than EXEC_ONCE, after you sync, emphatic will be running again which will mean that you will need to repeat the above for every sync.